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PubMed2005

In vitro apatite formation and its growth kinetics on hydroxyapatite/polyetheretherketone biocomposites.

The formation of biologically equivalent carbonate-containing apatite on the surface of synthetic hydroxyapatite (HA) is an important step leading to good bone healing. In this study, HA-reinforced polyetheretherketone (PEEK) composites were prepared by homogeneous mixing of HA and PEEK powders, compaction, and pressureless sintering. The bioactivity of HA/PEEK composite with 10, 20, 30 and 40 vol% HA was evaluated by immersing the composite disks in the simulated body fluid (SBF) for up to 4 weeks. The surface of composite with 40 vol% HA was covered by a layer of bone-like apatite just after 3 days of immersion, while 10 vol% HA was covered only after 28 days. This apatite layer was characterized by SEM, thin film X-ray diffractometer, attenuated total reflectance-Fourier transform infrared spectrometer (FTIR)/FTIR. Introducing a concept called apatite-forming capacity of SBF, growth kinetics of the apatite layer on the surface of the composite disks was carried out. The growth rate constant increased with HA volume fraction of the composite, suggesting that the bioactivity of the HA/PEEK composite increases with increasing HA volume fraction in the composite.

Apatites↗
PubMed2005

Deconfinement phase transition in a 3D nonlocal U(1) lattice gauge theory.

We introduce a 3D compact U(1) lattice gauge theory having nonlocal interactions in the temporal direction, and study its phase structure. The model is relevant for the compact QED3 and strongly correlated electron systems like the t-J model of cuprates. For a power-law decaying long-range interaction, which simulates the effect of gapless matter fields, a second-order phase transition takes place separating the confinement and deconfinement phases. For an exponentially decaying interaction simulating matter fields with gaps, the system exhibits no signals of a second-order transition.

Journal Article↗
PubMed1996

Initial evaluation of an interactive test of sentence gist recognition.

The laser videodisc-based Sentence Gist Recognition (SGR) test consists of sets of topically related sentences that are cued by short film clips. Clients respond to test items by selecting picture illustrations and may interact with the talker by using repair strategies when they do not recognize a test item. The two experiments, involving 40 and 35 adult subjects, respectively, indicated that the SGR may better predict subjective measures of speechreading and listening performance than more traditional audiologic sentence and nonsense syllable tests. Data from cochlear implant users indicated that the SGR accounted for a greater percentage of the variance for selected items of the Communication Profile for the Hearing-Impaired and the Speechreading Questionnaire for Cochlear-Implant Users than two other audiologic tests. As in previous work, subjects were most apt to ask the talker to repeat an utterance that they did not recognize than to ask the talker to restructure it. It is suggested that the SGR may reflect the interactive nature of conversation and provide a simulated real-world listening and/or speechreading task. The principles underlaying this test are consistent with the development of other computer technologies and concepts, such as compact discinteractive and virtual reality.

Adult↗
PubMed1996

Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations.

There are several knowledge-based energy functions that can distinguish the native fold from a pool of grossly misfolded decoys for a given sequence of amino acids. These decoys, which are typically generated by mounting, or "threading", the sequence onto the backbones of unrelated protein structures, tend to be non-compact and quite different from the native structure: the root-mean-squared (RMS) deviations from the native are commonly in the range of 15 to 20 angstroms. Effective energy functions should also demonstrate a similar recognition capability when presented with compact decoys that depart only slightly in conformation from the correct structure (i.e. those with RMS deviations of approximately 5 angstroms or less). Recently, we developed a simple yet powerful method for native fold recognition based on the tendency for native folds to form hydrophobic cores. Our energy measure, which we call the hydrophobic fitness score, is challenged to recognize the native fold from 2000 near-native structures generated for each of five small monomeric proteins. First, 1000 conformations for each protein were generated by molecular dynamics simulation at room temperature. The average RMS deviation of this set of 5000 was 1.5 angstroms. A total of 323 decoys had energies lower than native; however, none of these had RMS deviations greater than 2 angstroms. Another 1000 structures were generated for each at high temperature, in which a greater range of conformational space was explored (4.3 angstroms RMS deviation). Out of this set, only seven decoys were misrecognized. The hydrophobic fitness energy of a conformation is strongly dependent upon the RMS deviation. On average our potential yields energy values which are lowest for the population of structures generated at room temperature, intermediate for those produced at high temperature and highest for those constructed by threading methods. In general, the lowest energy decoy conformations have backbones very close to native structure. The possible utility of our method for screening backbone candidates for the purpose of modelling by side-chain packing optimization is discussed.

Protein Folding↗
PubMed2004

Modeling and simulation of intracellular dynamics: choosing an appropriate framework.

Systems biology is a reemerging paradigm which, among other things, focuses on mathematical modeling and simulation of biochemical reaction networks in intracellular processes. For most simulation tools and publications, they are usually characterized by either preferring stochastic simulation or rate equation models. The use of stochastic simulation is occasionally accompanied with arguments against rate equations. Motivated by these arguments, we discuss in this paper the relationship between these two forms of representation. Toward this end, we provide a novel compact derivation for the stochastic rate constant that forms the basis of the popular Gillespie algorithm. Comparing the mathematical basis of the two popular conceptual frameworks of generalized mass action models and the chemical master equation, we argue that some of the arguments that have been put forward are ignoring subtle differences and similarities that are important for answering the question in which conceptual framework one should investigate intracellular dynamics.

Algorithms↗
PubMed2005

Morphologic instability and cancer invasion.

PURPOSE: A solid tumor embedded in host tissue is a three-dimensional arrangement of cells and extracellular matrix that acts as a sink of oxygen and cell nutrients, thus establishing diffusional gradients. This and variations in vascular density and blood flow typically produce intratumoral regions of hypoxia and acidosis, and may result in spatially heterogeneous cell proliferation and migration. Here, we formulate the hypothesis that through these mechanisms, microenvironmental substrate gradients may drive morphologic instability with separation of cell clusters from the tumor edge and infiltration into surrounding normal tissue. EXPERIMENTAL DESIGN: We used computer simulations and in vitro experiments. RESULTS: We provide evidence that morphologic instability could be suppressed in vivo by spatially homogeneous oxygen and nutrient supply because normoxic conditions act both by decreasing gradients and increasing cell adhesion and, therefore, the mechanical forces that maintain a well-defined tumor boundary. A properly working tumor microvasculature can help maintain compact noninfiltrating tumor morphologies by minimizing oxygen and nutrient gradients. In contrast, antiangiogenic therapy, by increasing microenvironmental heterogeneity, may promote morphologic instability, leading to invasive patterns even under conditions in which the overall tumor mass shrinks. CONCLUSIONS: We conclude that therapeutic strategies focused solely on reduction of vascular density may paradoxically increase invasive behavior. This theoretical model accounts for the highly variable outcome of antiangiogenic therapy in multiple clinical trials. We propose that antiangiogenic strategies will be more consistently successful when aimed at "normalizing" the vasculature and when combined with therapies that increase cell adhesion so that morphologic instability is suppressed and compact, noninvasive tumor morphologies are enforced.

Antineoplastic Agents↗
PubMed1995

Domains in folding of model proteins.

By means of Monte Carlo simulation, we investigated the equilibrium between folded and unfolded states of lattice model proteins. The amino acid sequences were designed to have pronounced energy minimum target conformations of different length and shape. For short fully compact (36-mer) proteins, the all-or-none transition from the unfolded state to the native state was observed. This was not always the case for longer proteins. Among 12 designed sequences with the native structure of a fully compact 48-mer, a simple all-or-none transition was observed in only three cases. For the other nine sequences, three states of behavior-the native, denatured, and intermediate states-were found. The contiguous part of the native structure (domain) was conserved in the intermediate state, whereas the remaining part was completely unfolded and structureless. These parts melted separately from each other.

Amino Acid Sequence↗
PubMed2005

Comparison of small field of view gamma camera systems for scintimammography.

OBJECTIVE: To compare the performance characteristics of three compact gamma camera systems for scintimammography. METHODS: A multi-crystal NaI system (Dilon 6800), a multicrystal CsI system (Digirad 2020tc Imager) and a prototype cadmium zinc telluride (CZT) detector were evaluated using a breast phantom with simulated tumours of 1.8-9.8 mm in diameter and a tumour to background ratio of 5.6 : 1. A conventional Anger-based gamma camera was also evaluated for comparative purposes. RESULTS: The conventional gamma camera had the highest intrinsic sensitivity of the four systems and utilized the highest resolution collimator. However, the prototype CZT and the CsI systems yielded the best spatial resolution over the range 0-5 cm from the collimator face and better visualized small (5-7 mm) tumours. CONCLUSION: In addition to the advantage of close proximity to the breast, two of the three compact detectors offered superior performance to a conventional gamma camera for scintimammography.

Breast↗
PubMed1992

Effects of compact volume and chain stiffness on the conformations of native proteins.

An investigation of the statistical properties of the native conformations of proteins, observed from crystal structures, is reported. Protein conformations were analyzed in terms of a bond vector correlation function and molecular volume. It was observed that, while the volume of a protein structure varies nearly linearly with the number of residues, the bond vector correlation function exhibits a universal feature for all sizes of proteins. To interpret the nature of the bond vector correlation function of native protein structures quantitatively, Monte Carlo simulations of realistic polypeptide chains of specific but arbitrary amino acid sequence were carried out. The molecule was constrained in an ellipsoidal volume determined by its chain length, and conformations with unacceptable nonbonded contacts between different amino acid residues were excluded. The interactions within a terminally blocked single residue, which correlate two nearest-neighbor peptide groups in a chain, were taken into account by an energetically biased sampling of its phi-psi space. The simulated chain correlation functions were found to be in good agreement with those of the crystal structures of beta-sheet-type and mixed-type (alpha+beta) proteins of similar length. On the basis of these calculations, it is concluded that the observed conformations of these native proteins may arise from two basic factors: the compactness of structures under hydrophobic interactions and the intrinsic stiffness of polypeptide chains due to the interactions within each terminally blocked residue.

Biophysical Phenomena↗
PubMed1998

Folding of the human protein FKBP. Lattice Monte-Carlo simulations.

Monte-Carlo simulations of folding of the human protein FKBP are presented. The protein is confined in a simple cubic lattice and only nearest-neighbour interactions are considered. The evolution of protein structure, energy and diameter is followed over time. Starting from different extended conformations, compact globular forms with a hydrophobic core are reached above a critical temperature Tc, while below Tc the protein 'freezes' into high-energy, non-compact states. In the temperature range of folding, all the recorded intermediate states belong to two structural groups, where the process spends most of its time, separated by relatively fast transitions. During folding, the protein is successively composed of three and two compact fragments, whose separation occurs at loop positions. From comparisons performed on a domain of the family sharing 24% identity with FKBP, it appears that the number of fragments, and therefore their location, are sequence dependent.

Amino Acid Sequence↗
PubMed1995

Is burst hydrophobic collapse necessary for protein folding?

Folding of the lattice model of proteins is studied using Monte Carlo simulation. The amino acid sequence is designed to have a pronounced energy minimum for a given target (native) conformation. Our simulations reveal two possible scenarios. When the overall attraction between residues dominates, we find that folding to the native conformation is preceded by a rapid collapse into a burst intermediate which is a compact but structureless globule. Then, after a much longer time, an all-or-none transition from the globule to the native conformation occurs. In contrast, when the overall attraction is not strong, we do not observe a burst collapse stage. Instead, we find an all-or-none transition directly from the coil to the native conformation. Both scenarios yield comparable rates of folding. On the basis of these findings we discuss the role of intermediates in thermodynamics and kinetics of protein folding.

Amino Acid Sequence↗
PubMed2000

Salt-dependent compaction of di- and trinucleosomes studied by small-angle neutron scattering.

Using small-angle neutron scattering (SANS), we have measured the salt-dependent static structure factor of di- and trinucleosomes from chicken erythrocytes and from COS-7 cells. We also determined the sedimentation coefficients of these dinucleosomes and dinucleosomes reconstituted on a 416-bp DNA containing two nucleosome positioning sequences of the 5S rDNA of Lytechinus variegatus at low and high salt concentrations. The internucleosomal distance d was calculated by simulation as well as Fourier back-transformation of the SANS curves and by hydrodynamic simulation of sedimentation coefficients. Nucleosome dimers from chicken erythrocyte chromatin show a decrease in d from approximately 220 A at 5 mM NaCl to 150 A at 100 mM NaCl. For dinucleosomes from COS-7 chromatin, d decreases from 180 A at 5 mM to 140 A at 100 mM NaCl concentration. Our measurements on trinucleosomes are compatible with a compaction through two different mechanisms, depending on the salt concentration. Between 0 and 20 mM NaCl, the internucleosomal distance between adjacent nucleosomes remains constant, whereas the angle of the DNA strands entering and leaving the central nucleosome decreases. Above 20 mM NaCl, the adjacent nucleosomes approach each other, similar to the compaction of dinucleosomes. The internucleosomal distance of 140-150 A at 100 mM NaCl is in agreement with distances measured by scanning force microscopy and electron microscopy on long chromatin filaments.

Animals↗
PubMed1992

Optimal protocol and trajectory visualization for conformational searches of peptides and proteins.

Conformational searches by molecular dynamics and different types of Monte Carlo or build-up methods usually aim to find the lowest-energy conformation. However, this is often misleading, as the energy functions used in conformational calculations are imprecise. For instance, though positions of local minima defined by the repulsive part of the Lennard-Jones potential are usually altered only slightly by functional modification, the relative depths of the minima could change significantly. Thus, the purpose of conformational searches and, correspondingly, performance criteria should be reformulated and appropriate methods found to extract different local minima from the search trajectory and allow visualization in the search space. Attempts at convergence to the lowest-energy structure should be replaced with efforts to visit a maximum number of different local energy minima with energies within a certain range. We use this quantitative criterion consistently to evaluate performances of different search procedures. To utilize information generated in the course of simulation, a "stack" of low energy conformations is created and stored. It keeps track of variables and visit numbers for the best representatives of different conformational families. To visualize the search, projection of multidimensional walks onto a principal plane defined by a set of reference structures is used. With Met-enkephalin as a structural example and a Monte Carlo procedure combined with energy minimization (MCM) as a basic search method, we analyzed the influence on search efficiency of different characteristics as temperature schedules, the step size for variable modification, constrained random step and response mechanisms to search difficulties. Simulated annealing MCM had comparable efficiency with MCM at constant and elevated temperature (about 600 K). Constraining the randomized choice of side-chain chi angles to optimal values (rotamers) on every MCM step did not improve, but rather worsened, the search efficiency. Two low-energy Met-enkephalin conformations with parallel Tyr1 and Phe4 rings, a gamma-turn around the Gly2 residue, and Phe4 and Met5 side-chains forming together a compact hydrophobic cluster were found and are suggested as possible structural candidates for interaction with a receptor or a membrane.

Amino Acid Sequence↗
PubMed1988

A numerical method for simulating the dynamics of human walking.

This paper presents a general method for simulating the movement of the lower extremity during human walking. It is based upon two separate algorithms: one for single support (an open kinematic chain), and the other for the double support phase (a closed-loop linkage). Central to each of these is the recursive Newton-Euler inverse dynamics algorithm, applicable, as given, to any serial, spatial linkage. For the unconstrained single support model, the Newton-Euler scheme is applied directly to numerically generate the equations of motion. In the case of double support, however, the kinematic constraint equations are used to first eliminate the redundant degrees of freedom, and then solve for the unknown ground reactions under the constrained limb. The attractiveness of the method is that it offers a compact alternative to manually deriving the equations defining a mathematical model for human gait.

Algorithms↗
PubMed1996

The native state of apomyoglobin described by proton NMR spectroscopy: the A-B-G-H interface of wild-type sperm whale apomyoglobin.

Proton nuclear magnetic resonance spectroscopy was applied to sperm whale apomyoglobin to describe the conformation adopted by the protein under native conditions. The study focused on the A-B-G-H interface, a region known to form a compact subdomain in the apoprotein (Hughson and Baldwin, Biochemistry 28:4415-4422, 1989). Two histidine residues located in this subdomain, His24 and His119, interact and are thought to play a role in the acid denaturation process (Barrick et al., J. Mol. Biol. 237:588-601, 1994). A stable double mutant at these positions (His24Val/His119Phe sperm whale apomyoglobin) was compared with wild-type apomyoglobin. The amino acid replacements result in chemical shift perturbations near the mutations, in particular in the AB interhelical region, and in a deceleration of backbone amide hydrogen exchange in the B helix from position 27 to position 33. The double mutant data were used to expand and confirm the wild-type spectral analysis. Signals from the D helix were identified that demonstrate the formation of holoprotein-like structure. The assigned wild-type nuclear Overhauser effects, although in small number, were sufficient to construct a model of the compact subdomain of the apoprotein. This was achieved by using the structure of the holoprotein and restraining it with the geometrical information on the apoprotein in a simulated annealing procedure. The experimental restraints define a low-resolution model of the A-B-G-H interface in apomyoglobin.

Animals↗
PubMed2007

A knowledge-based move set for protein folding.

The free energy landscape of protein folding is rugged, occasionally characterized by compact, intermediate states of low free energy. In computational folding, this landscape leads to trapped, compact states with incorrect secondary structure. We devised a residue-specific, protein backbone move set for efficient sampling of protein-like conformations in computational folding simulations. The move set is based on the selection of a small set of backbone dihedral angles, derived from clustering dihedral angles sampled from experimental structures. We show in both simulated annealing and replica exchange Monte Carlo (REMC) simulations that the knowledge-based move set, when compared with a conventional move set, shows statistically significant improved ability at overcoming kinetic barriers, reaching deeper energy minima, and achieving correspondingly lower RMSDs to native structures. The new move set is also more efficient, being able to reach low energy states considerably faster. Use of this move set in determining the energy minimum state and for calculating thermodynamic quantities is discussed.

Glycine↗
PubMed2000

Structural and Transport Properties of Alumina Porous Membranes from Process-Based and Statistical Reconstruction Techniques.

We study the structural and transport properties of two model porous membranes made by compaction of spherical monosize gamma-alumina particles. A ballistic deposition process of spherical particles has been employed as a process-based representation method for accurately simulating the pore structure of the membranes. Comparison between the computed and experimental permeability values obtained in the Knudsen regime shows very good agreement for both membranes and indicates that sufficient representation of the original pore structure is achieved with the random sphere packs. In a further step, a medium with the same porosity and autocorrelation function as the sphere pack has been stochastically reconstructed. Comparison between the structural properties of the random sphere pack system (process-based model) and the stochastically reconstructed medium (statistical model) shows nearly identical correlation functions and pore chord length distributions but widely different mass chord length distributions. This is reflected to a significant difference in the prediction of a dynamic property like the Knudsen permeability by a factor of about 4. The results suggest that matching of the porosity and the two-point correlation function alone is not always adequate when pursuing an accurate representation of the structure of a porous material. In such cases, higher order statistical properties of the material contained in the chord length distribution of both pore and solid phase should be satisfied as well. It is also found that proper account of the formation process in the reconstruction of a porous material (process-based model) leads to representations of its structure more accurate than those of statistical reconstruction models. Copyright 2000 Academic Press.

Journal Article↗